Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g00954.F2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4333
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Found at i:488 original size:21 final size:21
Alignment explanation
Indices: 416--579 Score: 57
Period size: 21 Copynumber: 8.3 Consensus size: 21
406 CAAGGTCGCA
* * *
416 CACCACCTACACAAGCTCATT
1 CACCACCAACTCAAGCTCATC
*
437 CACCACCAACGCAA--T-A-C
1 CACCACCAACTCAAGCTCATC
* * *
454 CGCCCCCCACTCAAGCTCATC
1 CACCACCAACTCAAGCTCATC
* *
475 CACCACCTACTCAAGGT--TGC
1 CACCACCAACTCAAGCTCAT-C
* *
495 ACACCACCAACACAATTCTC-TC
1 -CACCACCAACTCAA-GCTCATC
*
517 CA-C-CC-ACTCAAGCTTATC
1 CACCACCAACTCAAGCTCATC
* ** *
535 CTCCACCAAGACAA--T-ACC
1 CACCACCAACTCAAGCTCATC
*
553 CACCACCTACTCAAGCTCATC
1 CACCACCAACTCAAGCTCATC
574 CACCAC
1 CACCAC
580 AAAGGCAATA
Statistics
Matches: 101, Mismatches: 27, Indels: 30
0.64 0.17 0.19
Matches are distributed among these distances:
17 12 0.12
18 21 0.21
19 7 0.07
20 6 0.06
21 52 0.51
22 2 0.02
23 1 0.01
ACGTcount: A:0.31, C:0.47, G:0.06, T:0.16
Consensus pattern (21 bp):
CACCACCAACTCAAGCTCATC
Found at i:541 original size:39 final size:39
Alignment explanation
Indices: 498--730 Score: 210
Period size: 39 Copynumber: 6.1 Consensus size: 39
488 AGGTTGCACA
** * * *
498 CCACCAACACAATTCTCTCCACCCACTCAAGCTTATCCT
1 CCACCAAGGCAATACTCGCCACCCACTCAAGCTCATCCT
* * * * *
537 CCACCAAGACAATACCCACCACCTACTCAAGCTCATCCA
1 CCACCAAGGCAATACTCGCCACCCACTCAAGCTCATCCT
* * * **
576 CCACAAAGGCAATACTCGCCACCCACTCAAACACATCAA
1 CCACCAAGGCAATACTCGCCACCCACTCAAGCTCATCCT
* * **
615 CCACCAATGCAATACT---CA-CCGC-CAA-CTCAAACT
1 CCACCAAGGCAATACTCGCCACCCACTCAAGCTCATCCT
*
648 CCACCAAGGCAATACCCGCCACCCACTCAAGCTCATCCT
1 CCACCAAGGCAATACTCGCCACCCACTCAAGCTCATCCT
* *
687 CCACCAAGGCAATTCTCGCCACCCACTCAAGGC-CATCCA
1 CCACCAAGGCAATACTCGCCACCCACTCAA-GCTCATCCT
726 CCACC
1 CCACC
731 CACACAAACT
Statistics
Matches: 156, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
33 17 0.11
34 3 0.02
35 3 0.02
36 4 0.03
37 3 0.02
38 3 0.02
39 121 0.78
40 2 0.01
ACGTcount: A:0.33, C:0.46, G:0.07, T:0.14
Consensus pattern (39 bp):
CCACCAAGGCAATACTCGCCACCCACTCAAGCTCATCCT
Found at i:578 original size:78 final size:75
Alignment explanation
Indices: 474--741 Score: 204
Period size: 78 Copynumber: 3.5 Consensus size: 75
464 TCAAGCTCAT
** * * *
474 CCACCACCTACTCAAGGTTGCACACCACCAACACAATTCTCTCCACCCACTCAAGCTTATCCTCC
1 CCACCACCTACTCAAGCAT-C-CACCACCAACACAATACTCGCCACCCACTCAAGCTCATCCTCC
539 ACCAAGACAATAC
64 ACCAAG-CAATAC
* ** * * **
552 CCACCACCTACTCAAGCTCATCCACCACAAAGGCAATACTCGCCACCCACTCAAACACATCAACC
1 CCACCACCTACTCAAG--CATCCACCACCAACACAATACTCGCCACCCACTCAAGCTCATCCTCC
617 ACCAATGCAATAC
64 ACCAA-GCAATAC
* * * * ** *
630 TCACCGCCAACTCAA--A--CTCCACCAAGGCAATACCCGCCACCCACTCAAGCTCATCCTCCAC
1 CCACCACCTACTCAAGCATCCACCACCAACACAATACTCGCCACCCACTCAAGCTCATCCTCCAC
*
691 CAAGGCAATTC
66 CAA-GCAATAC
* * * *
702 TCGCCACCCACTCAAGGCCATCCACCACCCACACAA-ACTC
1 CCACCACCTACTCAA-G-CATCCACCACCAACACAATACTC
742 ATCCTCCACC
Statistics
Matches: 149, Mismatches: 32, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
72 59 0.40
74 1 0.01
76 1 0.01
77 3 0.02
78 82 0.55
79 2 0.01
80 1 0.01
ACGTcount: A:0.33, C:0.46, G:0.07, T:0.14
Consensus pattern (75 bp):
CCACCACCTACTCAAGCATCCACCACCAACACAATACTCGCCACCCACTCAAGCTCATCCTCCAC
CAAGCAATAC
Found at i:715 original size:72 final size:77
Alignment explanation
Indices: 516--729 Score: 224
Period size: 72 Copynumber: 2.8 Consensus size: 77
506 ACAATTCTCT
* * * * *
516 CCACCCACTCAAGCTTATCCTCCACCAAGACAATACCCACCACCTACTCAAGCTCATCCACCACA
1 CCACCCACTCAAGCTCATCCTCCACCAAGGCAATACTCACCACCAACTCAA-CACATCCACCACA
*
581 AAGGCAATACTCG
65 AAGGCAATACCCG
* * ** * *
594 CCACCCACTCAAACACATCAACCACCAATGCAATACTCACCGCCAACTCAA-AC-TCCA-C-C-A
1 CCACCCACTCAAGCTCATCCTCCACCAAGGCAATACTCACCACCAACTCAACACATCCACCACAA
654 AGGCAATACCCG
66 AGGCAATACCCG
* * *
666 CCACCCACTCAAGCTCATCCTCCACCAAGGCAATTCTCGCCACCCACTCAAGGC-CATCCACCAC
1 CCACCCACTCAAGCTCATCCTCCACCAAGGCAATACTCACCACCAACTCAA--CACATCCACCAC
730 CCACACAAAC
Statistics
Matches: 109, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
72 54 0.50
73 1 0.01
74 2 0.02
75 8 0.07
76 2 0.02
77 1 0.01
78 41 0.38
ACGTcount: A:0.33, C:0.46, G:0.08, T:0.14
Consensus pattern (77 bp):
CCACCCACTCAAGCTCATCCTCCACCAAGGCAATACTCACCACCAACTCAACACATCCACCACAA
AGGCAATACCCG
Found at i:760 original size:99 final size:99
Alignment explanation
Indices: 646--829 Score: 242
Period size: 99 Copynumber: 1.9 Consensus size: 99
636 CCAACTCAAA
* * * * * *
646 CTCCACCAAGGCAATACCCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATTCTCGCCACCC
1 CTCCACCAAGGCAATACCCACCACCCACACAAGCTCATCCACCACCAACGCAATACCCGCCACCC
* *
711 ACTCAAGGCCATCCACCACCCACACAAACTCATC
66 ACCCAAAGCCATCCACCACCCACACAAACTCATC
* * * *
745 CTCCACCAATGCAATATCCACCACCTACACAAGCTCATTCACCACCAACGCAATACCCGCCACCC
1 CTCCACCAAGGCAATACCCACCACCCACACAAGCTCATCCACCACCAACGCAATACCCGCCACCC
**
810 ACCCAAATTCATCCACCACC
66 ACCCAAAGCCATCCACCACC
830 TACTCAAGGT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
99 71 1.00
ACGTcount: A:0.31, C:0.48, G:0.07, T:0.14
Consensus pattern (99 bp):
CTCCACCAAGGCAATACCCACCACCCACACAAGCTCATCCACCACCAACGCAATACCCGCCACCC
ACCCAAAGCCATCCACCACCCACACAAACTCATC
Found at i:764 original size:39 final size:39
Alignment explanation
Indices: 721--904 Score: 140
Period size: 39 Copynumber: 4.6 Consensus size: 39
711 ACTCAAGGCC
* *
721 ATCCACCACCCACACAAACTCATCCTCCACCAATGCAAT
1 ATCCACCACCCACACAAACTCATCCACCACCAACGCAAT
* * *
760 ATCCACCACCTACACAAGCTCATTCACCACCAACGCAAT
1 ATCCACCACCCACACAAACTCATCCACCACCAACGCAAT
* * * * * *
799 ACCCGCCACCCACCCAAATTCATCCACCACCTACTCAAGGT
1 ATCCACCACCCACACAAACTCATCCACCACCAACGCAA--T
* * * *
840 -TGCACACCACCTACTCAAGCTCATCCACCACCAA--CAAA
1 AT-C-CACCACCCACACAAACTCATCCACCACCAACGCAAT
* *
878 ATCCTCACCACCCACTCAATCTCATCC
1 AT-C-CACCACCCACACAAACTCATCC
905 TCCCTCACCA
Statistics
Matches: 114, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
39 85 0.75
40 3 0.03
41 2 0.02
42 24 0.21
ACGTcount: A:0.33, C:0.47, G:0.04, T:0.16
Consensus pattern (39 bp):
ATCCACCACCCACACAAACTCATCCACCACCAACGCAAT
Found at i:788 original size:60 final size:60
Alignment explanation
Indices: 666--790 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
656 GCAATACCCG
* * * *
666 CCACCCACTCAAGCTCATCCTCCACCAAGGCAATTCTCGCCACCCACTCAAGGCCATCCA
1 CCACCCACACAAACTCATCCTCCACCAAGGCAATTCTCACCACCCACACAAGGCCATCCA
* * *
726 CCACCCACACAAACTCATCCTCCACCAATGCAATATC-CACCACCTACACAA-GCTCATTCA
1 CCACCCACACAAACTCATCCTCCACCAAGGCAAT-TCTCACCACCCACACAAGGC-CATCCA
786 CCACC
1 CCACC
791 AACGCAATAC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 2 0.04
60 52 0.93
61 2 0.04
ACGTcount: A:0.30, C:0.48, G:0.06, T:0.15
Consensus pattern (60 bp):
CCACCCACACAAACTCATCCTCCACCAAGGCAATTCTCACCACCCACACAAGGCCATCCA
Found at i:868 original size:21 final size:21
Alignment explanation
Indices: 666--1036 Score: 104
Period size: 21 Copynumber: 18.2 Consensus size: 21
656 GCAATACCCG
*
666 CCACCCACTCAAGCTCATCCT
1 CCACCCACTCAAGCTCATCCA
* ** * *
687 CCACCAAGGCAA-TTC-T-CG
1 CCACCCACTCAAGCTCATCCA
705 CCACCCACTCAAGGC-CATCCA
1 CCACCCACTCAA-GCTCATCCA
* * *
726 CCACCCACACAAACTCATCCT
1 CCACCCACTCAAGCTCATCCA
*
747 CCA-CCAATGCAA--T-ATCCA
1 CCACCCACT-CAAGCTCATCCA
* * *
765 CCACCTACACAAGCTCATTCA
1 CCACCCACTCAAGCTCATCCA
* * * *
786 CCACCAACGCAA--T-ACCCG
1 CCACCCACTCAAGCTCATCCA
* **
804 CCACCCACCCAAATTCATCCA
1 CCACCCACTCAAGCTCATCCA
* *
825 CCACCTACTCAAGGT--TGCACA
1 CCACCCACTCAAGCTCAT-C-CA
*
846 CCACCTACTCAAGCTCATCCA
1 CCACCCACTCAAGCTCATCCA
* ** *
867 CCA-CCA-ACAAAATCCT-CA
1 CCACCCACTCAAGCTCATCCA
*
885 CCACCCACTCAATCTCATCCTCCCTCA
1 CCACCCACTCAAGCTCA---T--C-CA
*
912 CCACCCACTCAAGCTCATCCT
1 CCACCCACTCAAGCTCATCCA
* ** *
933 CCACCAAGACAA--T-ACCCA
1 CCACCCACTCAAGCTCATCCA
951 CCACCCACTCAAGCTCATCCA
1 CCACCCACTCAAGCTCATCCA
* ** *
972 CCACCAAGGCAA--T-A-CTCG
1 CCACCCACTCAAGCTCATC-CA
* *
990 CCACCCACTCAAACACATCCA
1 CCACCCACTCAAGCTCATCCA
* * *
1011 CCACCCACACAAACTCATCCT
1 CCACCCACTCAAGCTCATCCA
1032 CCACC
1 CCACC
1037 AAGGCAGTAC
Statistics
Matches: 250, Mismatches: 66, Indels: 68
0.65 0.17 0.18
Matches are distributed among these distances:
17 1 0.00
18 60 0.24
19 18 0.07
20 18 0.07
21 129 0.52
22 3 0.01
23 2 0.01
24 1 0.00
27 18 0.07
ACGTcount: A:0.32, C:0.49, G:0.05, T:0.15
Consensus pattern (21 bp):
CCACCCACTCAAGCTCATCCA
Found at i:910 original size:27 final size:27
Alignment explanation
Indices: 880--934 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
870 CCAACAAAAT
*
880 CCTCACCACCCACTCAATCTCATCCTC
1 CCTCACCACCCACTCAAGCTCATCCTC
907 CCTCACCACCCACTCAAGCTCATCCTC
1 CCTCACCACCCACTCAAGCTCATCCTC
934 C
1 C
935 ACCAAGACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.56, G:0.02, T:0.20
Consensus pattern (27 bp):
CCTCACCACCCACTCAAGCTCATCCTC
Found at i:922 original size:66 final size:66
Alignment explanation
Indices: 844--970 Score: 193
Period size: 66 Copynumber: 1.9 Consensus size: 66
834 CAAGGTTGCA
* *
844 CACCACCTACTCAAGCTCATCCACCACCAACAAAAT-CCTCACCACCCACTCAATCTCATCCTCC
1 CACCACCCACTCAAGCTCATCCACCACCAACAAAATACC-CACCACCCACTCAAGCTCATCCTCC
908 CT
65 CT
* * *
910 CACCACCCACTCAAGCTCATCCTCCACCAAGACAATACCCACCACCCACTCAAGCTCATCC
1 CACCACCCACTCAAGCTCATCCACCACCAACAAAATACCCACCACCCACTCAAGCTCATCC
971 ACCACCAAGG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 53 0.96
67 2 0.04
ACGTcount: A:0.31, C:0.50, G:0.03, T:0.16
Consensus pattern (66 bp):
CACCACCCACTCAAGCTCATCCACCACCAACAAAATACCCACCACCCACTCAAGCTCATCCTCCC
T
Found at i:953 original size:39 final size:39
Alignment explanation
Indices: 910--1015 Score: 158
Period size: 39 Copynumber: 2.7 Consensus size: 39
900 CATCCTCCCT
*
910 CACCACCCACTCAAGCTCATCCTCCACCAAGACAATACC
1 CACCACCCACTCAAGCTCATCCACCACCAAGACAATACC
* *
949 CACCACCCACTCAAGCTCATCCACCACCAAGGCAATACT
1 CACCACCCACTCAAGCTCATCCACCACCAAGACAATACC
* * *
988 CGCCACCCACTCAAACACATCCACCACC
1 CACCACCCACTCAAGCTCATCCACCACC
1016 CACACAAACT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.33, C:0.50, G:0.06, T:0.11
Consensus pattern (39 bp):
CACCACCCACTCAAGCTCATCCACCACCAAGACAATACC
Found at i:1015 original size:60 final size:60
Alignment explanation
Indices: 948--1621 Score: 377
Period size: 60 Copynumber: 11.1 Consensus size: 60
938 AAGACAATAC
* * * *
948 CCACCACCCACTCAAGCTCATCCACCACCAAGGCAATACTCGCCACCCACTCAAACACAT
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACAT
* * *
1008 CCACCACCCACACAAACTCATCCTCCACCAAGGCAGTACCCACCGCCCACTCAAACACAT
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACAT
** *
1068 CCACCACCAATGCAATACTCACCGCCAACTCAAACTCCACCAAGGCAATACCCGCCACCCACTCA
1 CCACCACC----C---ACTCA-----AACTCATCCTCCACCAAGGCAATACCCACCACCCACTCA
* *
1133 AGCTCAT
54 AACACAT
* * ** * * *
1140 CCTCCACCAAGGCAATACTCA-CCACCCACTCAAGGCCAT--CCACCACCCATTCAAACACAT
1 CCACCACCCACTCAA-ACTCATCC-TCCAC-CAAGGCAATACCCACCACCCACTCAAACACAT
* * * * * * *
1200 CCTCCACCATTAATGCAATACCCA-CCACCCACTCAA-ACACAT--CCACCACCAACTC-AA-AC
1 CCACCACC--CACT-CAA-ACTCATCC-TCCAC-CAAGGCA-ATACCCACCACCCACTCAAACAC
1259 -T
59 AT
* ** ** ** * ** *
1260 CCTCCACAAAGGCAATAC-CCGCCACCCACTCAA-GC--TCATTCACCACCCACTCAAGGC-CAT
1 CCACCACCCACTCAA-ACTCATCC-TCCAC-CAAGGCAAT-ACCCACCACCCACTCAA-ACACAT
* ** * * * * *
1320 CCGCCACCCACTCAAGTTTATCCTCCACCAAGGCAATACTCGCCACCCACTCAAGGC-TAT
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATACCCACCACCCACTCAA-ACACAT
* * * *
1380 CCACCACCAACTCAAA--C-TCCTCCACAAAGGCAATACCCGCCACCCACTCAAGGC-CAT
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATACCCACCACCCACTCAA-ACACAT
* ** * * *
1437 CCGCCACCCACTCAAGTTCATCCTCCACCAAGGCAATACCCACCACCCATTCAAGCTCAT
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACAT
* * * *
1497 CCACCACCTACACAAACTCACCCTCCACCAAGGCAATGCCCACCACCCACTCAAACACAT
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACAT
* *
1557 CCACCACCAACTCAAA--C-TCCTCCACCAAGGCAATACCCGCCACCCACTCAAACACAT
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACAT
1614 CCACCACC
1 CCACCACC
1622 AAAGCTATAC
Statistics
Matches: 494, Mismatches: 85, Indels: 73
0.76 0.13 0.11
Matches are distributed among these distances:
54 1 0.00
56 1 0.00
57 125 0.25
58 6 0.01
59 10 0.02
60 240 0.49
61 12 0.02
62 12 0.02
63 33 0.07
64 1 0.00
65 3 0.01
67 4 0.01
72 46 0.09
ACGTcount: A:0.32, C:0.48, G:0.07, T:0.13
Consensus pattern (60 bp):
CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATACCCACCACCCACTCAAACACAT
Found at i:1051 original size:39 final size:39
Alignment explanation
Indices: 1008--1660 Score: 183
Period size: 39 Copynumber: 16.7 Consensus size: 39
998 TCAAACACAT
* *
1008 CCACCACCCACACAAACTCATCCTCCACCAAGGCAGTAC
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATAC
* * * *
1047 CCACCGCCCACTCAAACACATCCACCACCAATGCAATAC
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATAC
* * *
1086 TCACCGCCAACTC-AA---A--CTCCACCAAGGCAATAC
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATAC
* *
1119 CCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATAC
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATAC
* * * * **
1158 TCACCACCCACTCAAGGC-CATCCACCACCCATTCAA-AC
1 CCACCACCCACTCAA-ACTCATCCTCCACCAAGGCAATAC
* * * * ** *
1196 ACATCC-TCCAC-CATTAA-TGCAATACCCACCACCCACTCAAACAC
1 CCA-CCACCCACTCA--AACT-C-AT--CCTCCACCAAGGC-AATAC
* *
1240 ATCCACCACCAACTCAAA--C-TCCTCCACAAAGGCAATAC
1 --CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATAC
* * * *
1278 CCGCCACCCACTCAAGCTCATTCACCACCCACTCAAGGCCAT--
1 CCACCACCCACTCAAACTCA-T--CC-TCCAC-CAAGGCAATAC
* ** *
1320 CCGCCACCCACTCAAGTTTATCCTCCACCAAGGCAATAC
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATAC
* * * * **
1359 TCGCCACCCACTCAAGGCT-ATCCACCACCAACTCAA-AC
1 CCACCACCCACTCAA-ACTCATCCTCCACCAAGGCAATAC
* ** ** ** * *
1397 TCCTCCACAAAGGCAATAC-CCGCCACCCACTCAAGGCCAT--
1 -CCACCACCCACTCAA-ACTCATCC-TCCAC-CAAGGCAATAC
* **
1437 CCGCCACCCACTCAAGTTCATCCTCCACCAAGGCAATAC
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATAC
* * * * **
1476 CCACCACCCATTCAAGCTCATCCACCACCTACACAA-AC
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATAC
* * * * * ** *
1514 TCACC-CTCCAC-CAAGGC-AATGCCCACCACCCACTCAAACAC
1 CCACCAC-CCACTCAA-ACTCAT--CCTCCACCAAGGC-AATAC
*
1555 ATCCACCACCAACTCAAA--C-TCCTCCACCAAGGCAATAC
1 --CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATAC
* * * * *
1593 CCGCCACCCACTCAAACACATCCACCACCAAAGCTATAC
1 CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATAC
* * *
1632 CCACCACCTACTCAAGCTCATCCACCACC
1 CCACCACCCACTCAAACTCATCCTCCACC
1661 CACTGAAACA
Statistics
Matches: 457, Mismatches: 104, Indels: 106
0.69 0.16 0.16
Matches are distributed among these distances:
33 24 0.05
34 1 0.00
35 1 0.00
36 27 0.06
37 25 0.05
38 41 0.09
39 245 0.54
40 13 0.03
41 10 0.02
42 32 0.07
43 14 0.03
44 13 0.03
45 4 0.01
46 5 0.01
47 2 0.00
ACGTcount: A:0.32, C:0.47, G:0.07, T:0.13
Consensus pattern (39 bp):
CCACCACCCACTCAAACTCATCCTCCACCAAGGCAATAC
Found at i:1069 original size:99 final size:99
Alignment explanation
Indices: 910--1102 Score: 287
Period size: 99 Copynumber: 1.9 Consensus size: 99
900 CATCCTCCCT
* * * *
910 CACCACCCACTCAAGCTCATCCTCCACCAAGACAATACCCACCACCCACTCAAGCTCATCCACCA
1 CACCACCCACACAAACTCATCCTCCACCAAGACAATACCCACCACCCACTCAAACACATCCACCA
* *
975 CCAAGGCAATACTCGCCACCCACTCAAACACATC
66 CCAAGGCAATACTCACCACCAACTCAAACACATC
* * *
1009 CACCACCCACACAAACTCATCCTCCACCAAGGCAGTACCCACCGCCCACTCAAACACATCCACCA
1 CACCACCCACACAAACTCATCCTCCACCAAGACAATACCCACCACCCACTCAAACACATCCACCA
* *
1074 CCAATGCAATACTCACCGCCAACTCAAAC
66 CCAAGGCAATACTCACCACCAACTCAAAC
1103 TCCACCAAGG
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
99 83 1.00
ACGTcount: A:0.34, C:0.48, G:0.06, T:0.11
Consensus pattern (99 bp):
CACCACCCACACAAACTCATCCTCCACCAAGACAATACCCACCACCCACTCAAACACATCCACCA
CCAAGGCAATACTCACCACCAACTCAAACACATC
Found at i:1112 original size:72 final size:72
Alignment explanation
Indices: 1030--1172 Score: 205
Period size: 72 Copynumber: 2.0 Consensus size: 72
1020 CAAACTCATC
* * * *
1030 CTCCACCAAGGCAGTACCCACCGCCCACTCAAACACATCCACCACCAATGCAATACTCACCGCCA
1 CTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAAGGCAATACTCACCACCA
1095 ACTCAAA
66 ACTCAAA
* * * * *
1102 CTCCACCAAGGCAATACCCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACTCACCACCC
1 CTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAAGGCAATACTCACCACCA
1167 ACTCAA
66 ACTCAA
1173 GGCCATCCAC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.33, C:0.47, G:0.08, T:0.12
Consensus pattern (72 bp):
CTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAAGGCAATACTCACCACCA
ACTCAAA
Found at i:1183 original size:132 final size:132
Alignment explanation
Indices: 910--1237 Score: 317
Period size: 132 Copynumber: 2.4 Consensus size: 132
900 CATCCTCCCT
* * * * *
910 CACCACCCACTCAAGCTCATCCTCCACC-AA-GACAATACCCACCACCCACTCAAGCTCATCCAC
1 CACCACCCACTCAAACACATCCACCACCTAATG-CAATACCCACCACCAACTCAA----A--CTC
* * *
973 CACCAAGGCAATACTCGCCACCCACTCAAACACATCCACCACCCACACAAACTCATCCTCCACCA
59 CACCAAGGCAATACCCGCCACCCACTCAAACACATCCACCACCAACACAAACTCATCCCCCACCA
1038 AGGCAGTACC
124 AGGCAGTA-C
* * *
1048 CACCGCCCACTCAAACACATCCACCACC-AATGCAATACTCACCGCCAACTCAAACTCCACCAAG
1 CACCACCCACTCAAACACATCCACCACCTAATGCAATACCCACCACCAACTCAAACTCCACCAAG
* * * **
1112 GCAATACCCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACTCA-CCACCCACTCAAGGC
66 GCAATACCCGCCACCCACTCAAACACATCCACCACCAACACAA-ACTCATCC-CCCAC-CAAGG-
1176 CA-T-C
127 CAGTAC
* * *
1180 CACCACCCATTCAAACACATCCTCCACCATTAATGCAATACCCACCACCCACTCAAAC
1 CACCACCCACTCAAACACATCCACCACC--TAATGCAATACCCACCACCAACTCAAAC
1238 ACATCCACCA
Statistics
Matches: 160, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
132 73 0.46
133 9 0.06
134 7 0.04
135 26 0.16
138 44 0.28
139 1 0.01
ACGTcount: A:0.34, C:0.48, G:0.06, T:0.12
Consensus pattern (132 bp):
CACCACCCACTCAAACACATCCACCACCTAATGCAATACCCACCACCAACTCAAACTCCACCAAG
GCAATACCCGCCACCCACTCAAACACATCCACCACCAACACAAACTCATCCCCCACCAAGGCAGT
AC
Found at i:1200 original size:21 final size:21
Alignment explanation
Indices: 1159--1258 Score: 82
Period size: 21 Copynumber: 4.8 Consensus size: 21
1149 AGGCAATACT
*
1159 CACCACCCACTCAAGGC-CATC
1 CACCACCCACTCAA-ACACATC
*
1180 CACCACCCATTCAAACACATC
1 CACCACCCACTCAAACACATC
* * *
1201 CTCCA-CCA-TTAATGCA-ATACC
1 CACCACCCACTCAA-ACACAT--C
1222 CACCACCCACTCAAACACATC
1 CACCACCCACTCAAACACATC
*
1243 CACCACCAACTCAAAC
1 CACCACCCACTCAAAC
1259 TCCTCCACAA
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
19 5 0.08
20 6 0.10
21 42 0.67
22 5 0.08
23 5 0.08
ACGTcount: A:0.36, C:0.48, G:0.03, T:0.13
Consensus pattern (21 bp):
CACCACCCACTCAAACACATC
Found at i:1347 original size:21 final size:21
Alignment explanation
Indices: 1281--1720 Score: 104
Period size: 21 Copynumber: 22.2 Consensus size: 21
1271 GCAATACCCG
*
1281 CCACCCACTCAAGCTCATTCA
1 CCACCCACTCAAGCTCATCCA
*
1302 CCACCCACTCAAGGC-CATCCG
1 CCACCCACTCAA-GCTCATCCA
* * *
1323 CCACCCACTCAAGTTTATCCT
1 CCACCCACTCAAGCTCATCCA
* ** *
1344 CCACCAAGGCAA--T-A-CTCG
1 CCACCCACTCAAGCTCATC-CA
1362 CCACCCACTCAAGGCT-ATCCA
1 CCACCCACTCAA-GCTCATCCA
* * *
1383 CCACCAACTCAAACTCCTCCA
1 CCACCCACTCAAGCTCATCCA
* ** * *
1404 -CA--AAGGCAA--T-ACCCG
1 CCACCCACTCAAGCTCATCCA
*
1419 CCACCCACTCAAGGC-CATCCG
1 CCACCCACTCAA-GCTCATCCA
* *
1440 CCACCCACTCAAGTTCATCCT
1 CCACCCACTCAAGCTCATCCA
* ** *
1461 CCACCAAGGCAA--T-ACCCA
1 CCACCCACTCAAGCTCATCCA
*
1479 CCACCCATTCAAGCTCATCCA
1 CCACCCACTCAAGCTCATCCA
* * * * *
1500 CCACCTACACAAACTCACCCT
1 CCACCCACTCAAGCTCATCCA
* **
1521 CCACCAAGGCAA--TGC--CCA
1 CCACCCACTCAAGCT-CATCCA
* *
1539 CCACCCACTCAAACACATCCA
1 CCACCCACTCAAGCTCATCCA
* * *
1560 CCACCAACTCAAACTCCTCCA
1 CCACCCACTCAAGCTCATCCA
** * *
1581 CCA---AGGCAA--T-ACCCG
1 CCACCCACTCAAGCTCATCCA
* *
1596 CCACCCACTCAAACACATCCA
1 CCACCCACTCAAGCTCATCCA
1617 CCA-CCA---AAGCT-ATACCCA
1 CCACCCACTCAAGCTCAT--CCA
*
1635 CCACCTACTCAAGCTCATCCA
1 CCACCCACTCAAGCTCATCCA
* * *
1656 CCACCCACTGAAACACATCCA
1 CCACCCACTCAAGCTCATCCA
* *
1677 CCACCAACACAA--T-A-CTCA
1 CCACCCACTCAAGCTCATC-CA
*
1695 CCACCCACTCAAGCCCATCCA
1 CCACCCACTCAAGCTCATCCA
1716 CCACC
1 CCACC
1721 AAGGCAATAC
Statistics
Matches: 300, Mismatches: 77, Indels: 84
0.65 0.17 0.18
Matches are distributed among these distances:
15 7 0.02
16 6 0.02
17 5 0.02
18 70 0.23
19 6 0.02
20 11 0.04
21 184 0.61
22 9 0.03
23 2 0.01
ACGTcount: A:0.32, C:0.48, G:0.07, T:0.13
Consensus pattern (21 bp):
CCACCCACTCAAGCTCATCCA
Found at i:1405 original size:138 final size:139
Alignment explanation
Indices: 1158--1452 Score: 416
Period size: 138 Copynumber: 2.1 Consensus size: 139
1148 AAGGCAATAC
* *
1158 TCACCACCCACTCAAGGCCATCCACCACCCATTCAAACACATCCTCCACCATTAATGCAATACCC
1 TCACCACCCACTCAAGGCCATCCACCACCCACTCAAACACATCCTCCACC--TAAGGCAATACCC
1223 ACCACCCACTCAAACACATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACCCGCCACCCA
64 ACCACCCACTCAAACACATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACCCGCCACCCA
1288 CTCAA-GCTCAT
129 CTCAAGGC-CAT
* **** * *
1299 TCACCACCCACTCAAGGCCATCCGCCACCCACTCAAGTTTATCCTCCACC-AAGGCAATACTCGC
1 TCACCACCCACTCAAGGCCATCCACCACCCACTCAAACACATCCTCCACCTAAGGCAATACCCAC
* *
1363 CACCCACTCAAGGC-TATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACCCGCCACCCAC
66 CACCCACTCAA-ACACATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACCCGCCACCCAC
1427 TCAAGGCCAT
130 TCAAGGCCAT
* *
1437 CCGCCACCCACTCAAG
1 TCACCACCCACTCAAG
1453 TTCATCCTCC
Statistics
Matches: 139, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
138 92 0.66
139 3 0.02
141 44 0.32
ACGTcount: A:0.32, C:0.47, G:0.08, T:0.14
Consensus pattern (139 bp):
TCACCACCCACTCAAGGCCATCCACCACCCACTCAAACACATCCTCCACCTAAGGCAATACCCAC
CACCCACTCAAACACATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACCCGCCACCCACT
CAAGGCCAT
Found at i:1504 original size:138 final size:135
Alignment explanation
Indices: 1214--1483 Score: 348
Period size: 138 Copynumber: 2.0 Consensus size: 135
1204 CACCATTAAT
1214 GCAATACCCACCACCCACTCAAACACATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACC
1 GCAATA-CCACCACCCACTCAAACACATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACC
* * * * *
1279 CGCCACCCACTCAAGCTCATTCACCACCCACTCAAGGCCATCCGCCACCCACTCAAGTTTATCCT
65 CGCCACCCACTCAAGCTCATCCACCACCCACTCAAGGCCATCCGCCACCAACGCAA--TTACCCA
1344 CCACCAAG
128 CCACCAAG
* * *
1352 GCAATACTCGCCACCCACTCAAGGC-TATCCACCACCAACTCAAACTCCTCCACAAAGGCAATAC
1 GCAATAC-CACCACCCACTCAA-ACACATCCACCACCAACTCAAACTCCTCCACAAAGGCAATAC
* ** * *
1416 CCGCCACCCACTCAAGGC-CATCCGCCACCCACTCAAGTTCATCCTCCACCAAGGCAA-TACCCA
64 CCGCCACCCACTCAA-GCTCATCCACCACCCACTCAAGGCCATCCGCCACCAACGCAATTACCCA
1479 CCACC
128 CCACC
1484 CATTCAAGCT
Statistics
Matches: 116, Mismatches: 13, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
135 9 0.08
137 1 0.01
138 103 0.89
139 3 0.03
ACGTcount: A:0.31, C:0.47, G:0.09, T:0.13
Consensus pattern (135 bp):
GCAATACCACCACCCACTCAAACACATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACCC
GCCACCCACTCAAGCTCATCCACCACCCACTCAAGGCCATCCGCCACCAACGCAATTACCCACCA
CCAAG
Found at i:1525 original size:138 final size:139
Alignment explanation
Indices: 1221--1527 Score: 322
Period size: 138 Copynumber: 2.2 Consensus size: 139
1211 AATGCAATAC
* * *
1221 CCACCACCCACTCAAACACATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACCCGCCACC
1 CCACCACCTACACAAACTCATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACCCGCCACC
* * * * *
1286 CACTCAAGCTCATTCACCACCCACTCAAGGCCATCCGCCACCCACTCAAGTTTATCCTCCACCAA
66 CACTCAAGCTCATCCACCACCCACTCAAGGCCATCCGCCACCAACGCAA--TTACCCACCACCAA
1351 GGCAATACTCG
129 GGCAATACTCG
**
1362 CCACC-CACT-CA-AGGCT-ATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACCCGCCAC
1 CCACCAC-CTACACAAACTCATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACCCGCCAC
* ** * * *
1423 CCACTCAAGGC-CATCCGCCACCCACTCAAGTTCATCCTCCACCAAGGCAA-TACCCACCACCCA
65 CCACTCAA-GCTCATCCACCACCCACTCAAGGCCATCCGCCACCAACGCAATTACCCACCACCAA
** * *
1486 TTCAA-GCTCAT
129 GGCAATACTC-G
* *
1497 CCACCACCTACACAAACTCACCCTCCACCAA
1 CCACCACCTACACAAACTCATCCACCACCAA
1528 GGCAATGCCC
Statistics
Matches: 135, Mismatches: 24, Indels: 17
0.77 0.14 0.10
Matches are distributed among these distances:
134 3 0.02
135 20 0.15
136 3 0.02
137 3 0.02
138 94 0.70
139 4 0.03
140 2 0.01
141 6 0.04
ACGTcount: A:0.31, C:0.48, G:0.07, T:0.14
Consensus pattern (139 bp):
CCACCACCTACACAAACTCATCCACCACCAACTCAAACTCCTCCACAAAGGCAATACCCGCCACC
CACTCAAGCTCATCCACCACCCACTCAAGGCCATCCGCCACCAACGCAATTACCCACCACCAAGG
CAATACTCG
Found at i:1560 original size:18 final size:18
Alignment explanation
Indices: 1539--1618 Score: 54
Period size: 18 Copynumber: 4.3 Consensus size: 18
1529 GCAATGCCCA
1539 CCACCCACTCAAACACAT
1 CCACCCACTCAAACACAT
* *
1557 CCACCACCAACTCAAACTCCT
1 CCA-C-CC-ACTCAAACACAT
* ** **
1578 CCACCAAGGCAATAC-CCG
1 CCACCCACTCAA-ACACAT
1596 CCACCCACTCAAACACAT
1 CCACCCACTCAAACACAT
1614 CCACC
1 CCACC
1619 ACCAAAGCTA
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
17 2 0.04
18 24 0.52
19 4 0.09
20 3 0.07
21 13 0.28
ACGTcount: A:0.35, C:0.51, G:0.04, T:0.10
Consensus pattern (18 bp):
CCACCCACTCAAACACAT
Found at i:1639 original size:57 final size:56
Alignment explanation
Indices: 1341--1683 Score: 264
Period size: 60 Copynumber: 5.9 Consensus size: 56
1331 TCAAGTTTAT
* * * *
1341 CCTCCACCAAGGCAATACTCGCCACCCACTCAAGGC-TATCCACCACC-AACTCAAAC
1 CCTCCACCAAGGCAATACCCACCACCCACTCAA-ACACATCCACCACCAAACT-AAAC
* * * * * *
1397 TCCTCCACAAAGGCAATACCCGCCACCCACTCAAGGC-CATCCGCCACC-CACTCAAGTTCAT
1 -CCTCCACCAAGGCAATACCCACCACCCACTCAA-ACACATCCACCACCAAACT-AA----AC
* * * * *
1458 CCTCCACCAAGGCAATACCCACCACCCATTCAAGCTCATCCACCACCTACACAAACTCAC
1 CCTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACC-AAACTAA---AC
*
1518 CCTCCACCAAGGCAATGCCCACCACCCACTCAAACACATCCACCACC-AACTCAAAC
1 CCTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAAACT-AAAC
* *
1574 TCCTCCACCAAGGCAATACCCGCCACCCACTCAAACACATCCACCACCAAAGCTATAC
1 -CCTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAAA-CTAAAC
* * ** * *
1632 CCACCACCTACTCAAGCTCATCCACCACCCACTGAAACACATCCACCACCAA
1 CCTCCACCAAGGCAA--T-ACCCACCACCCACTCAAACACATCCACCACCAA
1684 CACAATACTC
Statistics
Matches: 243, Mismatches: 29, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
56 2 0.01
57 105 0.43
58 7 0.03
59 7 0.03
60 116 0.48
61 3 0.01
62 3 0.01
ACGTcount: A:0.33, C:0.48, G:0.07, T:0.12
Consensus pattern (56 bp):
CCTCCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCAAACTAAAC
Found at i:1657 original size:117 final size:117
Alignment explanation
Indices: 948--1693 Score: 446
Period size: 117 Copynumber: 6.4 Consensus size: 117
938 AAGACAATAC
* * ** * * ** * *
948 CCACCACCCACTCAAGCTCATCCACCACCAAGGCAATACT-CGCCACCCACTCAAACACATCCAC
1 CCACCACCCACTCAAACACATCCACCACCAACTCAATACTCCTCCACCAAGGC-AATAC--CCGC
* * * * * *
1012 CACCCACACAAACTCATCCTCCACCAAGGCAGTACCCACCGCCCACTCAAACACAT
63 CACCCACTCAAACTCATCCACCACCAAAGCA-TACCCACCACCCACTCAAGCTCAT
* * *
1068 CCACCA-CCAATGC-AATAC-T-CACCGCCAACTCAA-A---CTCCACCAAGGCAATACCCGCCA
1 CCACCACCCACT-CAAACACATCCACCACCAACTCAATACTCCTCCACCAAGGCAATACCCGCCA
* * * *
1125 CCCACTCAAGCTCATCCTCCACCAAGGCAATACTCACCACCCACTCAAGGC-CAT
65 CCCACTCAAACTCATCCACCACCAAAGC-ATACCCACCACCCACTCAA-GCTCAT
* * * * * ** *
1179 CCACCACCCATTCAAACACATCCTCCACCATTAATGCAATAC-CCACCACCCACTCAAACACATC
1 CCACCACCCACTCAAACACATCCACCACCA--ACT-CAATACTCCTCCACCAAGGC-AATAC--C
* * * * *
1243 CACCACCAACTCAAACTCCTCCA-CA--AAGGCAATACCCGCCACCCACTCAAGCTCAT
60 CGCCACCCACTCAAACTCATCCACCACCAAAGC-ATACCCACCACCCACTCAAGCTCAT
* * * * *
1299 TCACCACCCACTCAAGGC-CATCCGCCACCCACTCAAGTTTA-TCCTCCACCAAGGCAATACTCG
1 CCACCACCCACTCAA-ACACATCCACCACCAACTCAA---TACTCCTCCACCAAGGCAATACCCG
* ** * * ** ** *
1362 CCACCCACTCAAGGCT-ATCCACCACCAACTCAAACTCCTCCACAAAGGCAA--T-AC
62 CCACCCACTCAA-ACTCATCCACCACCAAAGCATAC-CCACCACCCACTCAAGCTCAT
* * * * * *
1416 CCGCCACCCACTCAAGGC-CATCCGCCACCCACTCAAGTTCATCCTCCACCAAGGCAATACCCAC
1 CCACCACCCACTCAA-ACACATCCACCACCAACTCAA-TAC-TCCTCCACCAAGGCAATACCCGC
* * * * * *
1480 CACCCATTCAAGCTCATCCACCACCTACA-CAAACTCACC-CTCCAC-CAAGGC-AAT
63 CACCCACTCAAACTCATCCACCACC-AAAGCATACCCACCAC-CCACTCAA-GCTCAT
1534 GCCCACCACCCACTCAAACACATCCACCACCAACTCAA-ACTCCTCCACCAAGGCAATACCCGCC
1 --CCACCACCCACTCAAACACATCCACCACCAACTCAATACTCCTCCACCAAGGCAATACCCGCC
* *
1598 ACCCACTCAAACACATCCACCACCAAAGCTATACCCACCACCTACTCAAGCTCAT
64 ACCCACTCAAACTCATCCACCACCAAAGC-ATACCCACCACCCACTCAAGCTCAT
* *
1653 CCACCACCCACTGAAACACATCCACCACCAACACAATACTC
1 CCACCACCCACTCAAACACATCCACCACCAACTCAATACTC
1694 ACCACCCACT
Statistics
Matches: 490, Mismatches: 91, Indels: 92
0.73 0.14 0.14
Matches are distributed among these distances:
111 57 0.12
112 10 0.02
113 5 0.01
114 14 0.03
115 5 0.01
116 12 0.02
117 193 0.39
118 28 0.06
119 22 0.04
120 118 0.24
121 5 0.01
122 2 0.00
123 19 0.04
ACGTcount: A:0.33, C:0.47, G:0.07, T:0.13
Consensus pattern (117 bp):
CCACCACCCACTCAAACACATCCACCACCAACTCAATACTCCTCCACCAAGGCAATACCCGCCAC
CCACTCAAACTCATCCACCACCAAAGCATACCCACCACCCACTCAAGCTCAT
Found at i:1659 original size:177 final size:177
Alignment explanation
Indices: 1274--1696 Score: 448
Period size: 177 Copynumber: 2.4 Consensus size: 177
1264 CACAAAGGCA
* * * * * * ** *
1274 ATACCCGCCACCCACTCAAGCTCATTCACCACCCACTCAAGGCCATCCGCCACCCACTCAAGTTT
1 ATACCCACCACCAACTCAAGCTCATCCACCACCCACTCAA-GCCATCCACCACCAACACAAACTC
* * * * *
1339 ATCCTCCACCAAGGCAATACTCGCCACCCACTCAAGGCTATCCACCACCAACTCAAACTCCTCCA
65 ACCCTCCACCAAGGCAATACCCACCACCCACTCAAGACCATCCACCACCAACTCAAACTCCTCCA
* *
1404 CAAAGGCAATACCCGCCACCCACTCAAGGCCATCCGCCACCCACTCAAGT
130 CAAAGGCAATACCCGCCACCCACTCAAGACCATCCACCACCCA--CAAGT
* * ** * * *
1454 -TCATCCTCCACCAAGGCAA--T-ACCCACCACCCATTCAAGCTCATCCACCACCTACACAAACT
1 AT-ACCCACCACCAACTCAAGCTCATCCACCACCCACTCAAGC-CATCCACCACCAACACAAACT
*
1515 CACCCTCCACCAAGGCAATGCCCACCACCCACTCAA-ACACATCCACCACCAACTCAAACTCCTC
64 CACCCTCCACCAAGGCAATACCCACCACCCACTCAAGAC-CATCCACCACCAACTCAAACTCCTC
*
1579 CACCAAGGCAATACCCGCCACCCACTCAA-ACACATCCACCA-CCA-AAGCT
128 CACAAAGGCAATACCCGCCACCCACTCAAGAC-CATCCACCACCCACAAG-T
* * *
1628 ATACCCACCACCTACTCAAGCTCATCCACCACCCACTGAAACACATCCACCACCAACACAATACT
1 ATACCCACCACCAACTCAAGCTCATCCACCACCCACTCAAGC-CATCCACCACCAACACAA-ACT
1693 CACC
64 CACC
1697 ACCCACTCAA
Statistics
Matches: 199, Mismatches: 34, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
173 3 0.02
174 13 0.07
175 1 0.01
176 8 0.04
177 153 0.77
178 8 0.04
179 1 0.01
180 12 0.06
ACGTcount: A:0.32, C:0.48, G:0.07, T:0.13
Consensus pattern (177 bp):
ATACCCACCACCAACTCAAGCTCATCCACCACCCACTCAAGCCATCCACCACCAACACAAACTCA
CCCTCCACCAAGGCAATACCCACCACCCACTCAAGACCATCCACCACCAACTCAAACTCCTCCAC
AAAGGCAATACCCGCCACCCACTCAAGACCATCCACCACCCACAAGT
Found at i:1670 original size:60 final size:60
Alignment explanation
Indices: 1476--1720 Score: 211
Period size: 60 Copynumber: 4.1 Consensus size: 60
1466 AAGGCAATAC
* * * * * * *
1476 CCACCACCCATTCAAGCTCATCCACCACCTACACAA-ACTCACC-CTCCAC-CAAGGCAAT
1 CCACCACCCACTCAAACACATCCACCACCAACACAATACCCACCAC-CCACTCAAGCCCAT
* * * * *
1534 GCCCACCACCCACTCAAACACATCCACCACCAACTCAA-A--CTCC-TCCAC-CAAGGCAAT
1 --CCACCACCCACTCAAACACATCCACCACCAACACAATACCCACCACCCACTCAAGCCCAT
* * * *
1591 ACCCGCCACCCACTCAAACACATCCACCACCAA-AGCTATACCCACCACCTACTCAAGCTCAT
1 --CCACCACCCACTCAAACACATCCACCACCAACA-CAATACCCACCACCCACTCAAGCCCAT
* *
1653 CCACCACCCACTGAAACACATCCACCACCAACACAATACTCACCACCCACTCAAGCCCAT
1 CCACCACCCACTCAAACACATCCACCACCAACACAATACCCACCACCCACTCAAGCCCAT
1713 CCACCACC
1 CCACCACC
1721 AAGGCAATAC
Statistics
Matches: 155, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
57 46 0.30
58 4 0.03
60 95 0.61
61 4 0.03
62 6 0.04
ACGTcount: A:0.34, C:0.50, G:0.04, T:0.11
Consensus pattern (60 bp):
CCACCACCCACTCAAACACATCCACCACCAACACAATACCCACCACCCACTCAAGCCCAT
Found at i:1697 original size:39 final size:39
Alignment explanation
Indices: 1654--1760 Score: 151
Period size: 39 Copynumber: 2.7 Consensus size: 39
1644 CAAGCTCATC
*
1654 CACCACCCACTGAAACACATCCACCACCAACACAATACT
1 CACCACCCACTCAAACACATCCACCACCAACACAATACT
* * **
1693 CACCACCCACTCAAGCCCATCCACCACCAAGGCAATACT
1 CACCACCCACTCAAACACATCCACCACCAACACAATACT
* *
1732 CGCCACCCATTCAAACACATCCACCACCA
1 CACCACCCACTCAAACACATCCACCACCA
1761 GTGCAATCCA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.36, C:0.49, G:0.05, T:0.10
Consensus pattern (39 bp):
CACCACCCACTCAAACACATCCACCACCAACACAATACT
Found at i:1756 original size:156 final size:156
Alignment explanation
Indices: 1104--1738 Score: 461
Period size: 156 Copynumber: 4.0 Consensus size: 156
1094 AACTCAAACT
* * * * * *
1104 CCACCAAGGCAATACCCGCCACCCACTCAAGCTCATCCTCCACCAAGGCAATACTCACCACCCAC
1 CCACCAAGGCAATACCAGCCACCCACTCAAACACATCCACCACCAAAGCAATACCCACCACCCAC
** * *
1169 TCAAGGC-CATCCACCACCCATTCAAACACATCCTCCACCATTA-ATGCAATACCCACCACCCAC
66 TCAA-GCTCATCCACCACCCACACAAACACACCCACCACCA--ACA--CAATACCCACCACCCAC
* *
1232 TCAAACACATCCACCACCAACTCAAACTCCT
126 TCAAACACATCCACCACCAACGCAAACTCCG
* * * * * * *
1263 CCACAAAGGCAATACCCGCCACCCACTCAAGCTCATTCACCACCCACTCAAGGCCAT--CCGCCA
1 CCACCAAGGCAATACCAGCCACCCACTCAAACACA-T--CCA-CCAC-CAAAGCAATACCCACCA
* * * * ** * * ** *
1326 CCCACTCAAGTTTATCCTCCACCAAGGCAATACTC-GCCACCCACTCAAGGC--TATCCACCACC
61 CCCACTCAAGCTCATCCACCACCCACACAA-ACACACCCA-CCAC-CAACACAATACCCACCACC
* * * *
1388 AACTC-AA-AC-TCCTCCACAAAGGCAATAC-CCG
123 CACTCAAACACATCCACCACCAACGCAA-ACTCCG
* *** * *
1419 CCACCCACTCAAGGCCAT-CC-GCCACCCACTCAAGTTCATCCTCCACCAAGGCAATACCCACCA
1 ----CCAC-CAAGGCAATACCAGCCACCCACTCAAACACATCCACCACCAAAGCAATACCCACCA
* * * * ** *
1482 CCCATTCAAGCTCATCCACCACCTACACAAACTCACCCTCCACCAAGGCAATGCCCACCACCCAC
61 CCCACTCAAGCTCATCCACCACCCACACAAACACACCCACCACCAACACAATACCCACCACCCAC
* *
1547 TCAAACACATCCACCACCAACTCAAACTCCT
126 TCAAACACATCCACCACCAACGCAAACTCCG
* * *
1578 CCACCAAGGCAATACCCGCCACCCACTCAAACACATCCACCACCAAAGCTATACCCACCACCTAC
1 CCACCAAGGCAATACCAGCCACCCACTCAAACACATCCACCACCAAAGCAATACCCACCACCCAC
** * * *
1643 TCAAGCTCATCCACCACCCACTGAAACACATCCACCACCAACACAATACTCACCACCCACTCAAG
66 TCAAGCTCATCCACCACCCACACAAACACACCCACCACCAACACAATACCCACCACCCACTCAAA
* *
1708 CCCATCCACCACCAAGGCAATACT-CG
131 CACATCCACCACCAACGCAA-ACTCCG
1734 CCACC
1 CCACC
1739 CATTCAAACA
Statistics
Matches: 379, Mismatches: 69, Indels: 59
0.75 0.14 0.12
Matches are distributed among these distances:
154 22 0.06
155 18 0.05
156 176 0.46
157 9 0.02
158 7 0.02
159 79 0.21
160 7 0.02
161 9 0.02
162 31 0.08
163 11 0.03
164 10 0.03
ACGTcount: A:0.33, C:0.47, G:0.07, T:0.13
Consensus pattern (156 bp):
CCACCAAGGCAATACCAGCCACCCACTCAAACACATCCACCACCAAAGCAATACCCACCACCCAC
TCAAGCTCATCCACCACCCACACAAACACACCCACCACCAACACAATACCCACCACCCACTCAAA
CACATCCACCACCAACGCAAACTCCG
Found at i:1758 original size:21 final size:21
Alignment explanation
Indices: 1596--1759 Score: 87
Period size: 21 Copynumber: 8.2 Consensus size: 21
1586 GCAATACCCG
1596 CCACCCACTCAAACACATCCA
1 CCACCCACTCAAACACATCCA
* * *
1617 CCA-CCA---AAGCTATACCCA
1 CCACCCACTCAAAC-ACATCCA
* * *
1635 CCACCTACTCAAGCTCATCCA
1 CCACCCACTCAAACACATCCA
*
1656 CCACCCACTGAAACACATCCA
1 CCACCCACTCAAACACATCCA
* * *
1677 CCACCAACAC-AATAC-T-CA
1 CCACCCACTCAAACACATCCA
* *
1695 CCACCCACTCAAGCCCATCCA
1 CCACCCACTCAAACACATCCA
* ** * *
1716 CCACCAAGGC-AATAC-T-CG
1 CCACCCACTCAAACACATCCA
*
1734 CCACCCATTCAAACACATCCA
1 CCACCCACTCAAACACATCCA
1755 CCACC
1 CCACC
1760 AGTGCAATCC
Statistics
Matches: 100, Mismatches: 32, Indels: 22
0.65 0.21 0.14
Matches are distributed among these distances:
17 3 0.03
18 26 0.26
19 10 0.10
20 11 0.11
21 46 0.46
22 4 0.04
ACGTcount: A:0.35, C:0.49, G:0.04, T:0.12
Consensus pattern (21 bp):
CCACCCACTCAAACACATCCA
Found at i:1767 original size:39 final size:38
Alignment explanation
Indices: 1656--1781 Score: 144
Period size: 39 Copynumber: 3.2 Consensus size: 38
1646 AGCTCATCCA
* ** *
1656 CCACCCACTGAAACACATCCACCACCAACACAATACTCA
1 CCACCCACTCAAACACATCCACCACC-AGGCAATACTCG
* *
1695 CCACCCACTCAAGCCCATCCACCACCAAGGCAATACTCG
1 CCACCCACTCAAACACATCCACCACC-AGGCAATACTCG
* * *
1734 CCACCCATTCAAACACATCCACCACCAGTGCAATCCACG
1 CCACCCACTCAAACACATCCACCACCAG-GCAATACTCG
1773 CCACCCACT
1 CCACCCACT
1782 AAAGGTTGCG
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
38 2 0.03
39 72 0.97
ACGTcount: A:0.34, C:0.48, G:0.06, T:0.11
Consensus pattern (38 bp):
CCACCCACTCAAACACATCCACCACCAGGCAATACTCG
Found at i:1777 original size:99 final size:96
Alignment explanation
Indices: 1521--1859 Score: 295
Period size: 99 Copynumber: 3.5 Consensus size: 96
1511 AACTCACCCT
* *
1521 CCACCAAGGCAATGCCCACCACCCACTCAAACACATCCACCACCAACT-CAA-ACTCCTCCACCA
1 CCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACC-ACTGCAACACTCCACCACCA
* * *
1584 AGGCAATACCCGCCACCCACTCAAACACATCCA
65 A-ACAATACCCACCACCCACTCAAGCACATCCA
* * * * * *
1617 CCACCAAAGCTATACCCACCACCTACTCAAGCTCATCCACCACCCACTGAAACACATCCACCACC
1 CCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCA-CCACTGCAACAC-TCCACCACC
* *
1682 AACACAATACTCACCACCCACTCAAGCCCATCCA
64 AA-ACAATACCCACCACCCACTCAAGCACATCCA
* * * * *
1716 CCACCAAGGCAATACTCGCCACCCATTCAAACACATCCACCACCAGTGCAATCCACGCCACCCAC
1 CCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCACTGCAA--CACTCCA-CCAC
* *** * ** * * * *
1781 TAAAGGTTGCGAACCACCTACTGAAGCTCATCCT
63 CAAACAATACCCACCACCCACTCAAGCACATCCA
* * * *
1815 CCACCGAGGCAATACTCACCTCCCACTCAAACTCATCCACCACCA
1 CCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCA
1860 TCCCAATACT
Statistics
Matches: 195, Mismatches: 41, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
96 39 0.20
97 4 0.02
98 9 0.05
99 134 0.69
100 9 0.05
ACGTcount: A:0.34, C:0.47, G:0.07, T:0.12
Consensus pattern (96 bp):
CCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCACCACTGCAACACTCCACCACCAA
ACAATACCCACCACCCACTCAAGCACATCCA
Found at i:1777 original size:138 final size:138
Alignment explanation
Indices: 1558--1883 Score: 358
Period size: 138 Copynumber: 2.4 Consensus size: 138
1548 CAAACACATC
* * *
1558 CACCACCAACTCAAA--C-TCCTCCACCAAGGCAATACCCGCCACCCACTCAAACACATCCACCA
1 CACCACCCACTCAAACCCATCCACCACCAAGGCAATACTCGCCACCCACTCAAACACATCCACCA
* * * *
1620 CCAAAGCTATACCCACCACCTACTCAAGCTCAT-C-CACCACCCACTGAAACACATCCACCACCA
66 CCAAAGCAATACCCACCACCCACTAAAGCT--TGCGAACCACCCACTGAAACACATCCACCACCA
1683 ACACAATACT
129 ACACAATACT
* *
1693 CACCACCCACTCAAGCCCATCCACCACCAAGGCAATACTCGCCACCCATTCAAACACATCCACCA
1 CACCACCCACTCAAACCCATCCACCACCAAGGCAATACTCGCCACCCACTCAAACACATCCACCA
** * * * * * * *
1758 CCAGTGCAAT-CCACGCCACCCACTAAAGGTTGCGAACCACCTACTGAAGCTCATCCTCCACCGA
66 CCAAAGCAATACC-CACCACCCACTAAAGCTTGCGAACCACCCACTGAAACACATCCACCACCAA
**
1822 GGCAATACT
130 CACAATACT
* * ***
1831 CACCTCCCACTCAAACTCATCCACCACCATCCCAATACTCGCCACCCACTCAA
1 CACCACCCACTCAAACCCATCCACCACCAAGGCAATACTCGCCACCCACTCAA
1884 GGTCGTACAC
Statistics
Matches: 158, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
135 13 0.08
136 1 0.01
137 4 0.03
138 140 0.89
ACGTcount: A:0.33, C:0.47, G:0.07, T:0.13
Consensus pattern (138 bp):
CACCACCCACTCAAACCCATCCACCACCAAGGCAATACTCGCCACCCACTCAAACACATCCACCA
CCAAAGCAATACCCACCACCCACTAAAGCTTGCGAACCACCCACTGAAACACATCCACCACCAAC
ACAATACT
Found at i:1874 original size:99 final size:99
Alignment explanation
Indices: 1693--1943 Score: 301
Period size: 99 Copynumber: 2.5 Consensus size: 99
1683 ACACAATACT
* * * *
1693 CACCACCCACTCAAGCCCATCCACCACCAAGGCAATACTCGCCACCCATTCAAACACATCCACCA
1 CACCACCTACTCAAGCTCATCCACCACCAAGGCAATACTCACCACCCACTCAAACACATCCACCA
* *
1758 CCAGTGCAATCCACGCCACCCACTAAAGGTTGCG-A
66 CCAGTCCAATACACGCCACCCACTAAAGG-T-CGTA
* * * * *
1793 -ACCACCTACTGAAGCTCATCCTCCACCGAGGCAATACTCACCTCCCACTCAAACTCATCCACCA
1 CACCACCTACTCAAGCTCATCCACCACCAAGGCAATACTCACCACCCACTCAAACACATCCACCA
* *
1857 CCA-TCCCAATACTCGCCACCCACTCAAGGTCGTA
66 CCAGT-CCAATACACGCCACCCACTAAAGGTCGTA
* * * *
1891 CACCACCTACTCAAGCTCATCCACCACCAACGCAACATTCACCGCCCACTCAA
1 CACCACCTACTCAAGCTCATCCACCACCAAGGCAATACTCACCACCCACTCAA
1944 GGTCATACGC
Statistics
Matches: 128, Mismatches: 20, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
97 2 0.02
98 3 0.02
99 123 0.96
ACGTcount: A:0.31, C:0.46, G:0.09, T:0.14
Consensus pattern (99 bp):
CACCACCTACTCAAGCTCATCCACCACCAAGGCAATACTCACCACCCACTCAAACACATCCACCA
CCAGTCCAATACACGCCACCCACTAAAGGTCGTA
Found at i:1896 original size:21 final size:21
Alignment explanation
Indices: 1872--1970 Score: 78
Period size: 21 Copynumber: 4.9 Consensus size: 21
1862 CCAATACTCG
*
1872 CCACCCACTCAAGGTCGTACA
1 CCACCCACTCAAGGTCATACA
* * *
1893 CCACCTACTCAAGCTCATCCA
1 CCACCCACTCAAGGTCATACA
* * *
1914 CCACCAACGCAA---CATTCA
1 CCACCCACTCAAGGTCATACA
* *
1932 CCGCCCACTCAAGGTCATACG
1 CCACCCACTCAAGGTCATACA
* *
1953 CCACCTACTCAAGTTCAT
1 CCACCCACTCAAGGTCAT
1971 CCATCACCAA
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
18 14 0.23
21 46 0.77
ACGTcount: A:0.29, C:0.43, G:0.10, T:0.17
Consensus pattern (21 bp):
CCACCCACTCAAGGTCATACA
Found at i:1903 original size:60 final size:60
Alignment explanation
Indices: 1839--2017 Score: 214
Period size: 60 Copynumber: 3.0 Consensus size: 60
1829 CTCACCTCCC
* * * *
1839 ACTCAAACTCATCCACCACCATCCCAATACTCGCCACCCACTCAAGGTCGTACACCACCT
1 ACTCAAGCTCATCCACCACCAACCCAATACTCGCCGCCCACTCAAGGTCATACACCACCT
* * * * *
1899 ACTCAAGCTCATCCACCACCAACGCAACATTCACCGCCCACTCAAGGTCATACGCCACCT
1 ACTCAAGCTCATCCACCACCAACCCAATACTCGCCGCCCACTCAAGGTCATACACCACCT
* * ** * * *
1959 ACTCAAGTTCATCCATCACCAAGTCAATACTTGCCGCCCACTCAAAGTCATCCACCACC
1 ACTCAAGCTCATCCACCACCAACCCAATACTCGCCGCCCACTCAAGGTCATACACCACC
2018 AATGCAGTAC
Statistics
Matches: 99, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 99 1.00
ACGTcount: A:0.30, C:0.44, G:0.08, T:0.17
Consensus pattern (60 bp):
ACTCAAGCTCATCCACCACCAACCCAATACTCGCCGCCCACTCAAGGTCATACACCACCT
Found at i:2041 original size:39 final size:40
Alignment explanation
Indices: 1953--2043 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 40
1943 AGGTCATACG
* **
1953 CCACCTACTC-AAGTTCATCCATCACCAAGTCAATACTTG
1 CCACCTACTCAAAGTTCATCCACCACCAAGTCAATACTCA
* * *
1992 CCGCCCACTCAAAG-TCATCCACCACCAA-TGCAGTACTCA
1 CCACCTACTCAAAGTTCATCCACCACCAAGT-CAATACTCA
2031 CCACCTACTCAAA
1 CCACCTACTCAAA
2044 TTATTCCGCA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
38 1 0.02
39 38 0.90
40 3 0.07
ACGTcount: A:0.32, C:0.41, G:0.08, T:0.20
Consensus pattern (40 bp):
CCACCTACTCAAAGTTCATCCACCACCAAGTCAATACTCA
Done.